Correct order for 'Color by Data Set' chart.

Refs #441.

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/style/EMStyleOptions.java

@@ -1,6 +1,6 @@
 package org.baderlab.csplugins.enrichmentmap.style;
 
-import java.util.Collection;
+import java.util.List;
 import java.util.Objects;
 
 import org.baderlab.csplugins.enrichmentmap.model.AbstractDataSet;
@@ -14,12 +14,12 @@ public class EMStyleOptions {
 	private final ChartOptions chartOptions;
 	private boolean postAnalysis;
 	private final boolean publicationReady;
-	private final Collection<? extends AbstractDataSet> dataSets;
+	private final List<? extends AbstractDataSet> dataSets;
 
 	/**
 	 * It is assumed that all the given DataSets come from the same EnrichmentMap.
 	 */
-	public EMStyleOptions(CyNetworkView networkView, EnrichmentMap map, Collection<? extends AbstractDataSet> dataSets,
+	public EMStyleOptions(CyNetworkView networkView, EnrichmentMap map, List<? extends AbstractDataSet> dataSets,
 			ChartOptions chartOptions, boolean postAnalysis, boolean publicationReady) {
 		this.networkView = Objects.requireNonNull(networkView);
 		this.map = Objects.requireNonNull(map);
@@ -37,7 +37,7 @@ public CyNetworkView getNetworkView() {
 		return networkView;
 	}
 
-	public Collection<? extends AbstractDataSet> getDataSets() {
+	public List<? extends AbstractDataSet> getDataSets() {
 		return dataSets;
 	}
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/control/ControlPanelMediator.java

@@ -15,6 +15,7 @@
 import java.awt.event.ItemEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
@@ -795,7 +796,16 @@ private EMStyleOptions createStyleOptions(EnrichmentMap map, EMViewControlPanel
 		if (map == null || viewPanel == null)
 			return null;
 
-		Set<AbstractDataSet> dataSets = viewPanel.getDataSetSelector().getCheckedItems();
+		Set<AbstractDataSet> checkedDataSets = viewPanel.getDataSetSelector().getCheckedItems();
+		
+		// Need to maintain the correct order
+		List<AbstractDataSet> dataSetList = new ArrayList<>();
+		for(AbstractDataSet ds : map.getDataSetList()) { // Need to maintain the same order that's in the EnrichmentMap object
+			if(checkedDataSets.contains(ds)) {
+				dataSetList.add(ds);
+			}
+		}
+		
 		boolean publicationReady = viewPanel.getPublicationReadyCheck().isSelected();
 		boolean postAnalysis = map.hasSignatureDataSets();
 
@@ -814,7 +824,7 @@ private EMStyleOptions createStyleOptions(EnrichmentMap map, EMViewControlPanel
 		boolean showLabels = viewPanel.getShowChartLabelsCheck().isSelected();
 		ChartOptions chartOptions = new ChartOptions(data, type, colorScheme, showLabels);
 
-		return new EMStyleOptions(viewPanel.getNetworkView(), map, dataSets, chartOptions, postAnalysis, publicationReady);
+		return new EMStyleOptions(viewPanel.getNetworkView(), map, dataSetList, chartOptions, postAnalysis, publicationReady);
 	}
 
 	private AssociatedStyleOptions createAssociatedStyleOptions(EnrichmentMap map, AssociatedViewControlPanel viewPanel) {